PaintOmics

PaintOmics integrates multi-omics datasets onto biological pathway maps to enable pathway-level integrative analysis and interpretation of gene expression, metabolite data, and regulatory layers.

Key Features:

• Integrative pathway mapping: Maps and integrates multi-omics datasets onto biological pathway maps for pathway-level analysis.
• Support for Multiple Pathway Databases: Integrates KEGG, Reactome, and MapMan pathway databases to provide pathway knowledge applicable to animal and plant studies.
• Traditional pathway-based enrichment and metabolite analysis: Augments pathway-based enrichment methods with metabolite-focused analyses to extend interpretation of metabolic changes.
• Metabolite Hub Analysis: Identifies compounds with a high number of significant genes within their network, suggesting regulation via gene expression changes.
• Metabolite Class Activity Analysis: Tests whether metabolic classes show a higher-than-expected proportion of significant elements, indicating class-level regulation under experimental conditions.
• Regulatory Omics Module: Analyzes trans-regulatory layers including microRNAs, transcription factors, and RNA-binding proteins to elucidate their contribution to pathway regulation.

Scientific Applications:

• Systems-level interpretation: Integrates gene expression, metabolite interactions, and regulatory layers to provide insights into complex biological networks.
• Cross-organism pathway analysis: Enables pathway-centric analyses applicable to both animal and plant studies using KEGG, Reactome, and MapMan.

Methodology:

Visualizes multi-omics data in the context of biological pathways and identifies significant patterns and regulatory interactions using computational methods.